Bonnie’s New Journey in Equestria
by JackieTheGamerGirl
Summary: After dying to something unknown to her, Bonnie is sent to Equestria to go on a journey through Equestria and save it. She will find out many things while she is here, mainly and unknown past that she must uncover to figure out her mystery between the Elements and if she is the untold seventh one. Is she the untold seventh Element of Harmony? Rated T for safety.
1. Sad end, New Beginning!

"Will I stop writing new fics?" The answer is no. Ok so basically this story is a Bonnie. She ends up in Equestria, after the prologue obviously. But let's get into it shall we :3.

 _In Lumiose City..._

 **Bonnie's POV.**

"My head hurts Clemont!" I tell him as he is trying to get me their as fast as he can. What had happened was is that, I got hit by something on the back of my neck, and now I have a huge headache.

"We're almost there, just five more minutes!" He yells back at me.

"Five?! I can probably only last another one!" I yell at him. I was probably going to pass out or something.

"Do you _need_ me to carry you?" He asks me as he stops and tries to help.

"Well I appreciate the effort," I tell him as I was going back and forth from conscience. I didn't know if I was gonna make it in time.

"I...can't... hold on...much... longer!" I barely get out as I started to loose grip of myself. I only saw white. I could hear muffled sounds, like crying.

"No, no! I won't lose you!" I could faintly hear Clemont say. Even if I may be still breathing and my heart is probably still beating, I have lost grip if my life. As I floated around in the light, I saw Arceus and another figure before me.

" _My my, young Bonnie. You had a sad end as I could tell. I would like you to meet someone._ " He told me. I looked at the figure next to him. It looked like a Rapidash, but not really at the same time.

" _This is Celestial, one of the two Princesses of Equestria._ " He explained. So it was a she, anyway. I looked at her for a moment.

"And why am I meeting her?" I ask looking back at Arceus.

" _You will find out more of your relationship with her. For now you are being put onto a new journey in Equestria, and shall be help protect like you once did here. For you, and few others, are worthy of coming here. They haven't arrived yet, so you are the first. Go on, warrior, and protect this land!_ " Arceus told me as a portal opened up. I took a deep breath and walked in. I did not expect this at all.

 _Somewhere in Ponyville_.

 **Twilight's POV**

"Come on Twilight just one more try!" Spike encouraged me. I was struggling to turn an apple into an orange. I was going to make my next attempt when.

"Twilight you might wanna read this." Spike told me as I walked over to my young assistant. He gave me the letter. It was from Celestia.

It said:

 _Dear Twilight,_

 _I would like you to help a new pony I have met here in Canterlot, I want you to teach her and make her a possible member of the Elements of Harmony. Her potential is unknown, so I will need you to send me a letter when you find something new about her._

 _Your faithful teacher,_

 _Princess Celestia_

So I have to Canterlot to meet some new pony. Well I now have something to do this weekend!

"Alright Spike were going to Canterlot!" I tell him as I pack a few things.

"What for? Do we need to take a test?" Spike asked me.

"No, were going to meet some new pony, that's all." I tell him as we head out the door to let our friends know.

"Well, why do we have to meet them?" Spike asked me.

"She says that they have a lot of unknown potential, and she could be a possible member of the Elements of Harmony. It seems unlikely since there are only six of them, but we'll see how it goes." I replied to him as we were walking to Sweet Apple Acres.

"Well, let's just hope they'll be okay with it." He said. I wonder who they may be.

 _In Celestia's castle._

 **Bonnie's POV.**

I woke up stretching my, wait, what do I have? Oh great, I got hooves for hands and feet. I saw Celestia again, this time looking out her window.

"You're awake, I'll teach you how to work your new body. It will take Twilight awhile to get here." She told me as she walked over to me.

"Here, let me help you up." She said as offered me her hoof. I took it and stood up.

"There are four types of ponies here in Equestria. There are the earth ponies, which deal with things related to the earth, such as animals and nature. Then there are the pegasi which can fly and control the weather all over Equestria. Then there are the unicorns, to where they use their magic to help both of the other tribes. Then the rarest of them all, are the alicorns, they are both unicorn and pegasus, only myself, my sister Luna, and Princess Cadence, who you will meet both later." Celestia explained to me.

"So, which one am I?" I ask her.

"You are a unicorn. Unicorns can learn spells, such as teleportain and telekinesis. You can also you can also use other spells, but you will find more about that later." She told me. I got excited, but before I fell because I wasn't paying attention if I was on the ground or not.

"Princess Celestia, I'm here! Now who did you want me to meet?" I heard someone say as a lavender pony with purple and magenta hair came in.

"Twilight I would like you to meet Bonnie. Bonnie this is my assistant Twilight." Celestia introduced us. We shook hooves, but didn't speak a word.

"Would you like to come back with me?" Twilight asked me.

"Sure." I replied. We walked all the way to a train station.

"So, how are you Twilight?" I finally ask after about ten minutes of silence. We boarded the train, when she finally spoke up.

"Good, I can't wait for my friends to meet you Bonnie. I wonder what Celestia meant when she said about your potential and becoming and Element of Harmony." Twilight told me.

"Can you explain to me what an Element of Harmony is?" I ask her.

"Sure thing!" She said as for the rest of the train ride was Twilight explaining to me about the Elements of Harmony, since apparently there is more than one. When we finally arrived at Ponyville, since that's where Twilight and her friends live, we got off and stretched our legs and went to go meet Twilight's friends.

"Hey guys, here she is!" Twilight catching all of her friends attentions. I hid behind her because I was for one, freaked out, and I was a bit shy. I wouldn't say I was the only one who was shy at that moment. A yellow pony with pink hair was hiding behind something as well, so we could be the same.

"Uh, Twilight, is she shy?" A orange pony asked Twilight.

"Um, I wouldn't say shy. I'd say scared. I've just never met so many ponies." I admitted to her coming from Twilight's back.

"Oh, well my name's Applejack. Nice to meet ya!" Applejack said. Then a pink pony came around me very fast putting some kind of hat on me.

"Uh..." I began when I was cut off by the pony who put the hat on me.

"Welcome! My name is Pinkie Pie, the best party pony in _all_ of Equestria!" Pinkie Pie said, while I took the hat off. Then the next thing I knew was rainbows surrounding me, with it then revealing a pony with rainbow hair.

"Name's Rainbow Dash, nice to meet ya. I am the fastest pegasus in Equestria, and my dream is to become a Wonderbolt!" Rainbow Dash told me. I wanted to ask what a Wonderbilt was, but I thought otherwise.

"Oh, well my name is Rarity. And darling, maybe this will make you look a bit better." Rarity said as she put a bow on my right ear.

"Uh thanks." I tell her. Then I approach the last one, the yellow one.

"M-my name is Fluttershy, and I talk to animals, and take care of them as well." Fluttershy told me.

"Well nice to meet you Fluttershy. And the rest of you as well. I think I'll have a great time here in Equestria!" I say proudly as we all laughed after the statement.

 **And that's it for chapter one of this story. No this doesn't tie in to the multiverse story. This is just a side story really. I will probably update this again tomorrow. But this Wednesday day, I won't update anything due to the fact I'm going to be traveling for six hours on a plane. So yea hope you enjoy and I'll see ya tomorrow for the next one. Peace!**


	2. First Day, a Nightmare and a Revelation

**So here chapter two for this story. Hope you enjoyed, and remember to RR! This chapter is in the past for part of it, but then we take a look at Bonnie's unknown connection to the Elements.**

 _Years ago..._

Celestia and Luna were excited to find out that they were going to have a younger sibling. When the day came, they were excited to meet their new sibling. Their mother, Stacey, came out with their new sibling wrapped in blankets.

"Is it a foal or a colt, Mother?" Luna asked impatiently, for she and Celestia waited months for this moment.

"Why, it's a foal, little Luna." Stacey replied to her younger daughter.

"What is her name?" Celestia asked, looking at the young foal in their mother's hooves.

"Her name is Bonnie, for she will be a beautiful princess like you and Luna." Stacey replied to her oldest daughter. For the three were enjoying time together, until their father, Alex, came in and gave bad news.

"We're under attack! Hide our baby and get Celestia and Luna out of here, now!" Alex yelled as he sent a thing of magic in front of him.

"Celestia and Luna you heard your father, go!" Stacey ordered as she and the siblings ran out of the area. They were running as fast as they could, until.

"No! Bonnie!" Stacey yelled, noticing Bonnie's disappearance.

"You two go on without me, I'll go find Bonnie!"

Instead of arguing they agreed with their mother and continued running through the castle trying to find the exit.

Stacey ran back for her youngest daughter, who she found with Alex.

"Take her and put her into that portal, it takes her to a world known as the Pokémon world. She will be find there!" Alex yelled and pointed to the mirror. Stacey put her through before saying, "I love you, and I hope you return to meet your unknown family. Goodbye!" She said crying as she put Bonnie through the portal and into the Pokémon world...

 _Present Time. Twilight's house._

Bonnie woke up in her new home in Equestria. The sun as beautiful as ever, lighting up her area. She had noticed that Twilight was awake.

"Hey Twilight, do you have a book about the Elements of Harmony?" She asked as she looked around the bookshelves.

"Yes, it is right here. And maybe you can learn some spells today." Twilight said handing Bonnie the book.

"Okay, maybe later. First I want to know more about them, with the information you gave me yesterday as well." She replied, going to an area.

"But, I'd like to try the telekinesis spell real quick." Bonnie said.

"It isn't a spell exactly, it's just natural for most unicorns. Teleportation is a spell however, so we can do that. And besides your using it right now!" Twilight said, pointing at the book Bonnie was magically holding.

"Oh, did not see that." Bonnie said rubbing the back of her head. She sat down on the floor and began reading about the Elements. She read until at a point it mentioned something about an untold Element.

"Hey Twilight, did you read this part?" Bonnie asked her. She came over and looked at the part Bonnie was reading.

"Yes, it seemed a bit confusing to me at first, but I understood it more when I kept reading." Twilight told her.

"Hmm, do you have a book about legends here in Equestria?" Bonnie asked putting her book down.

"Well, this book is similar to what you just said." Twilight said grabbing a book with her magic. She then gave the book to Bonnie.

"Thanks. I guess this'll work for now." Bonnie said as she took the book with her own magic.

"Hey Twilight, why don't we go see if Applejack needs help?" Spike asked getting the two's attentions.

"Sure, I'll look at these books later." Bonnie said putting the books down.

"Okay, then I guess let's go!" Twilight said as the three walked down to Sweet Apple Acres.

"Oh, howdy Twilight, Spike and Bonnie! How have y'all been?" Applejack asked as she came out to see the three, while wiping sweat off her face.

"We've been good, how has everything been for you?" Bonnie replied, looking around the area. (Okay I forgot to make her say her name in the last chapter, but just say they know Bonnie's name Okay? Anyway back to story).

"Same here sugar cube." Applejack replied. (By the way Bonnie is about the size of Applebloom. And this takes before the season two finale.)

"Hey Applejack who are you talking to outside?" A young foal asked coming out to see her big sister.

"Oh howdy Twilight, Spike! Who are you?" Applebloom asked Bonnie after greeting Twilight and Spike.

"My name is Bonnie, nice to meet you. Who are you?" Bonnie replied to her.

"Well my name is Applebloom! Nice to meet you Bonnie!" She said shaking her hoof.

"Well, you should probably go to school since you are Applebloom's age." Twilight suggested to Bonnie.

"I guess that'll be fine. I think for now let's help out Applejack!" Bonnie said as she got excited to help Applejack.

"Well Bonnie, I guess you and Applebloom can go buck some apple trees." Applejack said.

"I'll teach you how to buck, so don't worry!" Applebloom said as they went into the apple tree area.

"So what you do is simple. You just use your back two legs and kick one of these trees. I suggest you put this on, so you can catch the falling apples." Applebloom said, giving Bonnie a basket and put it on top of her back.

"Alright, that should be simple." Bonnie said as they went into bucking trees. It seemed very fun for Bonnie. Her basket soon got full, and had no idea what to do with it.

"When you basket gets full just put the apples into here." Applebloom said tapping her hoof on a wheel barrel. Bonnie put her apples in the barrel and went to go make more.

"Don't you think we should take a break?" Applebloom asked Bonnie.

"Oh, well I guess that's fine." Bonnie said as she went with Applebloom inside the barn.

"Wow, this is a big barn!" Bonnie admitted. She sat down as Applebloom got them both apple juices.

"And this apple juice is good!" Bonnie admitted again, amazed by the taste of the juice.

"Well, what do you think we make with a bunch of apples?" Applebloom asked her.

"Well I guess you make pies as well." Bonnie said.

"Well, your kinda right. But it's not all that we make." Applebloom replied. This confused Bonnie, but she decided to say nothing about it.

"Hey Bonnie, were about to leave, come on!" Twilight called.

"Gotta go, see you later Applebloom!" Bonnie said as she ran out of the barn.

"Well let's get going Twilight. So where are going?" Bonnie asked Twilight.

"We're going to Fluttershy's to go help her with the animals." Twilight replies to her.

"Well I'll race you to her place!" Bonnie said running off.

"Hey! You don't even know where her cottage is!" Twilight yelled running to catch up to her. Spike was gonna have one rough ride today.

"Well now I know what kind of house it is! Thanks!" Bonnie yelled Twilight. She stopped in front of the cottage and knocked on Fluttershy's door. Twilight just barely made it before Fluttershy opened her door.

"Well, you look exhausted." Fluttershy said as she gave them some water.

"Well, you can thank Bonnie for that. She thought it would be a good idea to race to your cottage." Twilight said.

"Hey! We didn't have to! I just wanted to run for a bit!" Bonnie yelled at her.

"Let's not get into an argument right now Okay." Twilight said.

"Okay." Bonnie said. Then they helped Fluttershy with the animals, by giving them baths and feeding them.

"Well where to next Twilight?" Bonnie said excited.

"Well, how about you get back to reading your books, so you can know more about Equestria." Twilight suggested.

"Okay, well can we get something to eat first?" Bonnie asked.

"Sure, let's get a table." Twilight said. Twilight and Bonnie got a table outside, as they waited for their drinks, they decided to figure out what they want to eat.

"I guess I'll try a daisy sandwich." Bonnie said as she put the menu down.

"Okay. Here come our drinks!" Twilight said as they both got their waters.

"What would you two like today?" The waiter asked them.

"A daisy sandwich for both of us please." Twilight told the waiter.

"It will be out in five minutes." The waiter said as he went inside to give the order.

"So, how are you liking Ponyville?" Twilight asked Bonnie.

"It's actually pretty nice here. It's very... never mind." Bonnie said before trailing off. She had realized she has told no one that she was originally from another world.

"Very what?" Twilight asked. Bonnie then realized she never pointed out her home, so she decided to continue her statement.

"Very calm, sorry I uh, side tracked." Bonnie said. Twilight didn't notice, but Bonnie was very nervous.

" _That was a close one. Only Celestia knows where I'm originally from._ " Bonnie thought.

"Bonnie?" Twilight said getting her attention. She had realized that their food had arrived. She grabbed the sandwich with her magic and took a bit, she was amazed how good it was.

"Is it good?" Twilight asked her. Bonnie nodded yes, still amazed by the taste. After about ten minutes they left and headed for the library. Once they got inside, Bonnie picked up one of the books she had been reading. She continued looking in the Legends of Equestria book when a certain part caught her attention.

"Hey Twilight have you read about this?" Bonnie asked.

"What is it Bonnie?" Twilight asked as she came over to see the part Bonnie was talking about.

It read:

 _A third unknown sibling to Celestia and Luna, and possibly the seventh element, is presumed dead. But some say not, for they think_ she _is still alive. Her whereabouts if she were alive, are unknown. For it is said that she will return in a thousand years, and fill the empty hole in Celestia and Luna's family._

"Wow, who knew that was a thing." Twilight admitted.

"Yeah, a missing sister, interesting. And she might me be the possible seventh element." Bonnie said.

" _What if I am that sister? I am the possible seventh element, as what I heard from Celestia, so it could make sense. But their alicorns and I'm not! Maybe I am part of their sister, I don't know this is all to confusing!_ "

Bonnie thought. The theory didn't add up to her, she knew she never lived in Equestria before, or did she. The thought made it even more confusing for her, she continued reading the book until she got done with. She studied _that_ legend, for it just confused her, a lot. She had trouble sleeping that night, because of the thought. She woke up and looked at the clock.

 _Half past one_

"Sigh, why can't I sleep! It's probably because of this stupid thought. Sigh, maybe I should get something to drink." She said to herself as she got up and got a glass of water.

"Sigh, I need to figure out why I have that thought, I'll probably talk to Twilight and the others tomorrow." She said to herself.

"Tell Twilight and the others about what?" Spike asked freaking Bonnie out.

"Sorry, you just scared me, and about a theory that I have." Bonnie explained to the purple dragon.

"What's it about?" Spike asked Bonnie.

"Sigh, it's about possibly me being that third sister, but it's a bit ridiculous. I am the possible seventh element, yes, but it doesn't add up. Their alicorns! I thought maybe I'm a part of her, but that made things even more confusing for me." She explained to Spike.

"Yeah, even I admit it doesn't add up. Why would you be her? Despite being the seventh element, it still doesn't make sense." Spike said.

"We should probably go back to sleep, or we'll be cranky tomorrow." Bonnie snickered at her joke as they went back to sleep.

"Night." They told each other before going back to sleep. Bonnie slept easy for the rest of the night, not having any complications with the theory that she thought about.

 _In her dream..._

Bonnie woke up and saw that Spike and Twilight weren't there. She checked upstairs, she then figured what happened.

"Must've slept in." She said to herself. She left the house and went to Sweet Apple Acres, and only saw Applejack there.

"Hey Applejack. Do you know where Twilight and Spike went?" Bonnie asked her. There was no response.

"Applejack? Hello?" She said as she got closer.

"Hello?" She said again before realizing she wasn't there.

"That's odd, well I guess I'll go hang out with Fluttershy, and maybe she'll know where the others went." She said to herself as she went along the path.

"Fluttershy? Do you know where Spike, Twilight and Applejack are? I can't find them anywhere!" Bonnie yelled as she ran towards the door. She knocked on it, before realizing it was unlocked.

"Uh, that's odd, but okay." She said as she walked in. No one was there, not even the animals.

"Where the heck is every pony?" She asked as she ran out of the house.

"Maybe, if I find Pinkie Pie, maybe she'll tell me what's going on!" She said as Bonnie ran to find Pinkie Pie.

"Pinkie Pie? Pinkie Pie! Applejack! Twilight! Spike! Fluttershy! Rarity! Rainbow Dash..." she trailed off before feeling like she was going to cry.

" _Now now, calm down little one, this is only a nightmare._ " A voice said, scaring Bonnie a bit.

"W-who are you?" Bonnie asked as it showed itself.

"I am Luna, and my job is to help ponies who are having nightmares." Luna explained.

"W-why am I having a nightmare?" Bonnie asked.

"Nightmares are based off of fear, and you are afraid of your friends leaving you." Luna told her.

"I-I'm not afraid of anything... I'm not...I'm... I'm." Bonnie trailed off.

"You _are_ afraid, everyone has some fears." Luna told her, calming her down.

"What is your name?" Luna asked.

"B-Bonnie, why do you ask?" Bonnie asked.

"Hm, it sounds familiar, I'm sorry for my departure for I need to Celestia something!" Luna said leaving Bonnie.

"Wait, come back!" She yelled before waking up.

"Gah!" She yelled as she woke up. She looked around, seeing Twilight and Spike.

"Something wrong Bonnie?" Twilight asked.

"Oh, uh, no. I'm fine." She said as she got up.

" _That's the first one since I've been here._ " Bonnie thought as she ate.

"Your gonna go with Applebloom today, so you can go to school. Remember you said you would yesterday." Twilight reminded her.

"Oh right. I guess it can't be so bad." She said as Twilight got her a few things for her first day.

 _Meanwhile with Celestia and Luna._

"Celestia!" Luna yelled as she flew in her sister's castle.

"Yes Luna." Celestia said in a calm voice.

"Do you know about..." Luna began before Celestia finished her statement.

"...that Bonnie has returned? Yes, but in her world she died. She protected with her friends there. Now she is here to help protect Equestria. She is with Twilight as we speak. She obviously doesn't remember since she was only a baby here. I hope Arceus can help her with a vision." Celestia explained to her younger sibling.

"Arceus reveals things in unexpected ways, remember." Luna reminded her.

"I know. I hope Mother and Father have been watching her in _there_ and here." Celestia admitted.

"I'm pretty sure they have been. There is no need to worry." Luna comforted Celestia.

 _In the Pokémon world..._

Clemont couldn't believe the news he had just received.

 _"Clemont, we couldn't save your sister in time, we're sorry."_ It echoed through his mind. Another voice was driving him insane, however.

" **Get rid of your friends. They did this to her! She can't be at peace until you get rid of them! She wants you to do it. She NEEDS you to do it!** " It kept saying every night. Clemont hated whatever was trying to him into killing his friends.

"Arceus, help me!" He'd whisper every night before sleeping, almost to no avail. He was losing his sanity every day, and resisted to battle anyone at the gym, and even go outside, because he'd know that he would snap, and be put in jail. At random times he would from crying to laughing like a maniac and back to crying all at the same time. Tonight was a different prayer then the rest.

"Arceus, why did you take her away from me! She could've done more! Is there a way I could see her again before I start killing people?" He asked, when for once, he got an answer.

"You can travel through a mirror in your home tomorrow morning and you will be able to see her for _one_ more day. This is a one time only thing however." Arceus said to him. Clemont didn't know what to say, he was in a deep thought. Then he got his answer.

"Tomorrow I'll do it tomorrow!" He said as he went to sleep. Little did he know, this wasn't actually Arceus, it was his insanity getting to him.

 **Ok, LOONNNG CHAPTER! Now what happened at the end here will be a different story, but hope you enjoyed chapter two! I may release chapter three today who knows. But see ya next time! Peace!**


	3. Learning a lot then expected!

**Yes, a third one. Anyway, remember in the last chapter towards the end we took a look at Clemont? Well, I will probably make it a side story. So basically, if I decided to, I will put some dialogue for this whole "Clemont lost his sanity." While it isn't going to be long, it will be interesting. But back to main story. Bonnie will meet the CMC, because why not? But she will also meet Diamond Tiara and Silver Spoon, but their before meeting CMC. Now let's get into chapter 3! And as you could tell by the last chapter I am improving, with more dialogue. Alright let me shut up, see you at the end! Peace!**

Bonnie was excited to see who she would meet at her new school. She met up with Applebloom, with her expression as the same as Bonnie's.

"Think we could hangout at my treehouse later? I have some ponies that would love to meet you!" Applebloom told Bonnie as it made her all the more happy.

"This is going to be an exciting day! I can't wait!" She said as she ran towards the school.

"Hey wait up!" Applebloom yelled as she ran to catch up to her. Bonnnie then stopped in front of the school, so Applebloom could catch up, and so she could catch her breath.

"Wow, you are fast!" Applebloom admitted as they entered the school. (Btw Twilight dealt with the thing so she could sign up for school.)

"Students, I think our new student has arrived. Would you like to introduce yourself to the class?" Mrs. Cheerile asked Bonnie. Bonnie got up from her seat, and walked to the front of her class.

"Hi my name is Bonnie, and I am a energetic pony. I like to race other ponies, even if they may be older than me." She said as she then heard some snickering. She decided not to let it bother her.

"I hope I can have an exciting time here with you all!" She finished as she went to her seat. After a few hours of class time, it was time for lunch. She grabbed her lunch and sat under a nearby tree. While she was eating, two ponies approached her.

"Hm? Is there something you need?" Bonnie asked the two before the pink one took her lunch.

"Hey, give that back!" She said as she used her magic to get her lunch back.

"Sorry, just wanted to see your reaction." The pink one said as she snickered.

"Who are you anyways?" She asked them.

"I am Diamond Tiara, and this is my friend Silver Spoon." Diamond Tiara said.

"So why did you take my lunch?" Bonnie asked.

"Oh Diamond Tiara look at her flank!" Silver Spoon said.

"Oh my Celestia, she's a blank flank!" Diamond Tiara said.

"What's wrong with that?" Bonnie asked.

"Let me tell you this, if you want to be cool like us, then get a cutie mark!" Diamond Tiara said, shoving Bonnie down.

"Hey! What was that for?" She yelled at them, getting up.

"Oh, well that was just for fun!" Silver Spoon said as she then shoved Bonnie to the tree.

"Stop it you guys, that hurts!" Bonnie said, on the verge of crying.

"What are you going to do, _cry for mommy_?

' _Mommy, daddy, help me these girls are bullying me!_ ' I'd like to see you try!" Diamond Tiara said mockingly.

"That's not funny!" Bonnie yelled at her. She was crying at this point.

"Wow, your a crybaby for being such a "energetic pony". Why don't they call you a sensitive pony instead? Hmm? Tell me why!" Silver Spoon said, as she and Diamond Tiara backed her into the tree.

"Leave me alone!" Bonnie said, with her next thing, being to climb into the tree.

"Wow, you're a crybaby and a scaredy cat? You must've been lying back there if this is how you really act?" Diamond Tiara said. Bonnie didn't leave the tree, she was to afraid.

"Bonnie? Bonnie? Where are you? Have you two seen Bonnie?" Applebloom asked them.

"She's up there." Silver Spoon said, pointing upwards in the tree.

"Bonnie, why are you up there?" Applebloom asked her.

"They were shoving me and making fun of me! I'm not coming down until they leave!" Bonnie yelled to Applebloom. Bonnie knew she had to get down eventually, but she was to afraid.

"Bonnie, you don't have to worry about them!" Applebloom yelled back at her.

"I'm not coming down!" She yelled back.

"Hey, what's wrong Applebloom?" A voice asked.

"Yeah, who are you talking to?" Another one asked.

"Scootaloo, Sweetie Belle, could you help me get Bonnie down.

"Who's that?" Sweetie Belle asked.

"She's our new friend. Diamond Tiara and Silver Spoon scared her so much that she went up the tree." Applebloom explained.

"Well let's help her out!" Scootaloo said.

"How are we going to get her down?" Sweetie Belle asked.

"Well, let's try to talk to her, see if we can calm her down." Scootaloo suggested.

"Hey Bonnie, my name is Scootaloo. I just want you to know that we can help you with your problem. Just come down and we can talk." Scootaloo said, as Bonnie slowly began to get down.

"You sure?" She asked when she finally got down.

"Yes." Scootaloo said as she took Bonnie to the others.

"It's Okay Bonnie. I'm Sweetie Belle, and we, the Cutie Mark Crusaders, will help you!" Sweetie Belle said.

"Who's the Cutie Mark Crusaders?" Bonnie asked.

"Well that's is!" Applebloom said.

"What do you do?" She asked.

"We basically find out many ways to try and get our Cutie Marks!" Sweetie Belle said.

"That sounds nice, is it okay if I join?" Bonnie asked.

"Sure! We always have room for one more!" Scootaloo said.

"Thanks!" Bonnie said, going back to her happy self.

"We should probably get back to class." Sweetie Belle suggested.

"Yea, then we could have our first meeting together!" Bonnie said as the four went back to class. When the day was done, Bonnie remembered something.

"Oh wait, I just remembered! I have to go back to Twilight's. Maybe I'll ask her if I can come over later. Should I tell her about the thing at lunch?" Bonnie said.

"Well, just say the truth. She'll understand! It's better then not telling her." Applebloom replies as Bonnie ran off.

"Bye guys! See ya later!" She yelled and waved to them.

"Bye!" They yelled back as they went their ways.

" _I just hope she won't freak out._ " She thought when she suddenly bumped into someone.

"Oof! Oh, sorry I didn't see you there." She apologized.

"It's okay, I forgive you. Just watch where you are going next time." The stallion told her, "I would like you to have this."

"Hm?" She said when she was then given an amulet by the stallion. She looked at it, confused.

"Why did you... give this to me?" She said when she saw that the stallion left.

"Well, that's... weird. Well, I guess just a nice guy." Bonnie said as she continued walking back to Twilight's. She walked in the door when she saw a note left on the table.

" _Dear Bonnie,_

 _You may notice Spike and I are not here. Well that is because, Spike and I had to head to Canterlot for a meeting with Celestia. You can go to Applejack's if you like. We may not be back until tomorrow afternoon. Hopefully you understand._

 _Your friend,_

 _Twilight._

After reading the note, Bonnie decided to head to Applejack's.

"Oh, what are you doing here suger cube?" Applejack asked her.

"Oh, Twilight and Spike are out in Canterlot because Celestia called a meeting. She told me I could stay here." Bonnie explained.

"Well, that's fine then. Ah don't mind you here." Applejack said to her, "If you want to find Applebloom, she's on her treehouse over there."

Applejack pointed to a yellow treehouse, near the barn.

"Okay, thanks!" Bonnie said as she went over to the treehouse.

"Oh hey Bonnie! Thought you were supposed to be with Twilight?" Applebloom asked her. Bonnie explained the meeting Twilight and Spike had to go to, and that she could stay at Applejack's.

"Well, then that's awesome! We could have a sleepover!" Applebloom said

"Don't you think we should start?" Sweetie Belle asked.

"Oh right. *Ahem, mayI announce our new member of the Cutie Mark Crusaders, Bonnie!" Applebloom said as then Sweetie Belle and Scootaloo throw a robe onto her back.

"Wow, this is a nice robe." Bonnie admitted.

"So what do you think we should do to find out Cutie Marks?" Applebloom asked, looking at Bonnie. Bonnie then realized that she was asking her.

"Oh, well I don't know." She admitted.

"Hey, where did you get that?" Scootaloo asked pointing to her amulet.

"Oh, uh, some nice pony gave it to me." She said as she held the amulet with her magic. She then put it back where it was. (Which was around her neck, it was kinda like a necklace.)

"Wow they must've been nice to give you something like that." Sweetie Belle said, amazed by its beauty.

"Oh why thanks!" Bonnie replied.

"So what do you wanna do to get our Cutie Marks?" Applebloom asked again.

"Oh, well I still don't know." Bonnie said before chuckling nervously. Little did she know this stallion was watching her. (And no not like a creep!)

 **???'s POV**

I didn't know she would show it to them first. Well, she's a filly, what would I expect. I gave her that amulet for a reason. She is the chosen one, the one that completes the puzzle to a mystery that plagued this land. Until now. She will prove her presence later, and that's when I will see her again. She may not know, but I do. I need to let her know that I have done it. For now, we shall wait.

 **Back to third person...**

After talking away most of the day, the CMC decided to call it a night.

"See you guys tomorrow!" Bonnie yelled as she waved to Sweetie Belle and Scootaloo, who were leaving.

"Bye! See you tomorrow!" They yelled back waving.

"Come on, let's go to bed!" Applebloom said excited.

"I don't think you can because you're so excited!" Bonnie told her.

"Yes I can!" She said, before realizing Bonnie was messing with her.

"Alright let's go." She said as she ran towards the barn. Once inside, Applebloom lead Bonnie to her room. Bonnie decided to sleep on the floor, knowing that Applebloom would feel comfortable in her own bed.

"Night." Bonnie said.

"Night." Applebloom said turning off the lamp.

 _In Bonnie's dream..._

"Ok this better not be a nightmare!" She said as she walked around the white room.

"Well where am I?" She asked as she continued walking.

" _Hello Bonnie._ " Arceus said as he made himself present.

"Oh, hi Arceus!" She said cheerfully.

" _Are you liking it so far?_ " He asked her.

"Yes! It is amazing here!" She said cheerfully.

" _You haven't told anyone yet, have you?_ " Arceus said. She didn't know what he was talking about, until she put two and two together.

"No, it that good or bad?" She asked.

" _Well that is good. They will find out later. I'm surprised you are cheerful. Aren't you trying to recover from today?_ " Arceus asked her.

"I don't want to talk about it." She said, after her mood changed almost immediately.

" _You don't have to, I already know. I know what happened._ " He said to her.

"So, why are you talking to me besides that anyways?" She asked him.

" _Well, sooner or later, you will have to face a challenge. I don't want what happened today to be block at that moment. And I want you to tell everyone in_ that _room why you are there and what happened to you back in my world._ " He said to her.

" _I must go, we will continue tomorrow._ " He said leaving. She then woke up.

"Gah! Why do I do that?" She asked as she got up.

"Do what?" Applebloom asked.

"Gah! Sorry, don't scare me like that. And it's nothing to worry about." She said grabbing her bag, "Let's go, we don't wanna be late! Race you!" Bonnie said as she started to run for school, practically skipping breakfast.

"Alright you're on!" Applebloom yelled, catching up to her. Once they got there, they decided to take a breather.

"You skipped breakfast, ya know?" Applebloom told Bonnie.

"I'll be fine." Bonnie told her.

"Hey girls! Why are you exhausted?" Scootaloo asked as she and Sweetie Belle arrived.

"I raced Applebloom." Bonnie said simply.

"Let's get in. Come on!" Sweetie Belle said as the four walked in. Lunch came by quick that day, and once they were outside, Bonnie went with Applebloom.

"Let me guess, you don't want them to bother you?" Applebloom said.

"Yea, after what happened yesterday, I do not want a repeat." Bonnie admitted.

"Don't worry we won't let them bother you!" Scootaloo said.

"Won't let who bother who?" Diamond Tiara asked, making Bonnie go behind Scootaloo.

"Oh, here's crybaby." Silver Spoon said.

"Hey! I am not a crybaby!" Bonnie yelled at her.

"Why can't you leave her alone?" Sweetie Belle asked them.

"Why do you think?" Silver Spoon replied.

"Come on Silver Spoon, we don't want a repeat of yesterday, now do we." Diamond Tiara, making Bonnie growl.

"Why are _you_ growling?" Silver Spoon asked.

"None of your business!" Bonnie yelled getting out from behind Scootaloo.

"Oh, so _now_ you're standing up? And I thought you were a real baby!" Diamond Tiara mocked her.

"Say one more word or else!" Bonnie threatened, filled with anger. This scared Diamond Tiara and Silver Spoon. Not just the threat, and also because here eyes were red and not the usual blue.

"Okay, I think we'll go now." Diamond Tiara as she and Silver Spoon ran.

"Hmpf! Sigh." Bonnie said, calming down.

"Did I scare you girls?" She asked.

"No, not really. Since when could you do that?" Applebloom asked.

"Do what?" Bonnie asked.

"You had red stuff surrounding your body, what was it?" Scootaloo asked, confusing Bonnie.

"I... don't know." She said. She didn't know that the red stuff was aura, activated by her anger.

"I'll talk to Twilight later about it." She said. She was fully calm now. She decided to stay quiet for the rest of the day, until she went back to Twilight's. Twilight was there today, so that made Bonnie calm down a bit more.

"Hey Bonnie! How was school today?" Twilight asked.

"Oh, good." She said calmly as she put her bag.

"How was school yesterday?" She asked.

"Good." Bonnie said again.

"Are you sure? You don't sound like it." Twilight said.

" _I don't know if I should tell her, I guess like Applebloom said, it's always good to be honest._ " Bonnie thought as she explained the events of the past two days at school.

"Red stuff surrounding you? And you don't even know what it is?" Twilight asked her.

"Yea." Bonnie said.

"It's a bit odd." Twilight said.

"I know, to be honest I didn't even know what I was doing at that moment. I was just mad and upset." Bonnie admitted.

"Maybe you can find it in a book. I think you might want to look in the Strange Powers book." Twilight suggested.

"I guess, but I just want to take a nap if that's okay with you." Bonnie said.

"Sure, I'll wake you up when dinner's ready." Twilight said.

"Thanks."

"No problem."

Bonnie then laid down on the ground and went to sleep.

" _Bonnie. Bonnie? Bonnie!_ " Arceus said making Bonnie get up.

"Yes Arceus." She said.

" _You're back a bit earlier then I expected._ " He said.

"Yea, I'm taking a nap." She told him.

"Can you tell me about the red stuff surrounding me earlier?" She asked him.

" _Oh that, well that is called aura._ " He started.

"Aura?"

" _Yes aura. It is something rare for people back in my world. It rarer here in Equestria. You will learn more once you look back in history. Anyway, Aura is spiritual energy in a physical form, such as Pokémon, people or ponies. You didn't have when you were in my world, but you apparently have it here. For some reason, it activated because of your rage. You were just lucky enough you didn't attack them. That would be going to a dangerous limit._ " He said.

" _Attack_ them?! Dangerous limit?! What are you talking about?" She asked him.

" _We will finish this later, for we must both go. See you tonight._ " He said leaving her.

"Wait!" She yelled before waking up.

"Ah! Oh, ok." She said as she got up.

"Why did you scream?" Spike asked her.

"Oh, that's been happening, and I don't know why." She told him.

"Oh, okay. I can understand. Well it's time to eat." Spike told her.

"Alright coming." Bonnie said. She felt a bit light headed when standing, but it went away quickly. She headed into the room and sat down to eat.

"So Bonnie, how was your nap?" Twilight asked her.

"Hm? Oh good." She told her.

"That's good." Twilight said as she ate.

" _I should've asked him about my amulet!_ " Bonnie thought. After eating, Bonnie stepped outside for a while so she could clear her head. Twilight came out moments later to see Bonnie sitting down.

"So, why did you come out here?" Twilight asked her.

"Well, I just needed to clear my head." Bonnie answered Twilight.

"You seemed very quiet while eating. Is there something you're not telling me? You don't have to tell me if that's the case." Twilight told her. Bonnie didn't know whether or not she should lie to Twilight.

"Well, no." Bonnie lied. She hated it with all her heart, but she needed to know later.

"Well maybe not now you'll tell me, but maybe later on." Twilight told her.

" _Must've thought that I lied. That makes sense at least._ " Bonnie thought. She then got up and went inside. Twilight followed, closing the door behind her.

"Let's get ready for bed." Bonnie said.

"Okay, night." Twilight told her.

"Night." She replied, as she went to bed.

" _So you're back?_ " Arceus asked.

"Yes, yes I am." She told him.

" _So you were wondering about some things earlier. Weren't you?_ " Arceus asked her.

"Yes." She replied.

" _Well I'm going to leave most of that untold._ " Arceus told her.

"Well do you know about the amulet I was given?" She asked, showing it to him.

" _Well, it has to do with your aura, and something in the near future. And if you are wondering, no, I will not tell you._ " Arceus told her.

"I understand." She told him.

" _We will talk soon._ " He told her.

"Wait, when?" She asked him.

" _Soon. Now go off into your dreams._ " He said as he drifted away from Bonnie.

"Wait! Gah, there's no point, he said soon. I can wait." She said as she entered a vision like dream.

"Where am I now?" She asked as she walked around.

"Well I guess I just look and do nothing. Wait what's happening?" She asked as she went to the doorway. She saw something, but as soon as she saw it, t went away and she woke up. This time she didn't yell, instead she just panted.

"What time is it?" She asked before looking at the clock.

 _Half past two._

"Oh great. I should just get some water then go back to sleep." She said as she got up. She went into the kitchen and got a glass of water. She drank it and went back to where she was sleeping, and went to sleep.

" _Let's hope today won't be bad. Wait, it's the weekend woohoo!_ " She thought as she went back to sleep.

 **The next morning.**

Bonnie woke up to the sunshine in her face. She went into the kitchen and saw Twilight and Spike with something.

"Oh, want to join us on our picnic with the others?" Twilight asked her.

"Sure!" She said as she came along. She smiled, happy to see them again.

"I'm here girls!" Twilight said as she greeted her friends.

"Hey Twilight!" Pinkie Pie said.

"What took you so long?" Rainbow Dash asked her.

"Goodness darling it shouldn't take that long to get here." Rarity said.

"Well I came along too." Bonnie said coming from behind Twilight.

"Oh hey Bonnie! How has it been?" The three asked her.

"Good!" She replied to them.

"Oh, hi Bonnie. I hope you're doing okay in school." Fluttershy said.

"Well... it's been..." Bonnie trailed off, not knowing what else to say.

"It's been what?" Rainbow asked her.

"Well, complicated." She finally said.

"How?" Pinkie Pie asked, while she was jumping all over the place.

"Well, I don't know how to explain it." She said before changing the subject, "How have you girls been?"

"Good as ever darling!" Rarity said.

"I've been doing my usual, getting faster and faster!" Rainbow Dash said.

"I've been making every pony smile!" Pinkie Pie said.

"I've been helping the animals." Fluttershy said.

"I've been around the farm." Applejack said.

"Well that's good!" Bonnie said. Then Spike burped up a note.

"Twilight, you might want to read this." Spike said giving it to Twilight.

Twilight was shocked when she got the letter.

 **Cliffhanger. MUWAHAHAHAHAHAHAHAHA!**

 **Anyway, hope you enjoyed another long chapter, took me two days to make. Love you all and I'll see you next time. Peace!**


	4. Saving Equestria Part One!

**Ok, so I wrote this while I was on my plane home. So we are of course going to find out what exactly the letter said. Hope you enjoyed this! Peace!**

When Twilight read the letter, she was shocked.

"Shining Armor is having a wedding?!" She said.

"What?!" Everyone yelled, confused. (Ok I'm pretty most of you guys saw this coming.)

"Wait, who is Shining Armor?" Bonnie asked.

"Shining Armor is my brother." Twilight explained.

"Oh, and why are you mad? Isn't that, like a good thing." Bonnie asked.

"Well, he hasn't talked to me in a while, and that he tells me now!" Twilight yelled.

"Well, did it say anything else?" Bonnie asked, wanting to change the subject.

"Oh, well I didn't read that far." Twilight said, continuing to read the paper she was sent.

 _Dear Twily,_

 _I need you and your friends' help with my wedding. I need Pinkie Pie to do the decorations for the party. Fluttershy can do the music for the wedding._ (Ok one thing, DONT ask me how he knows their names! I hate questions like that. It is a bit dumb for people to ask that, and it's pretty much pointless to ask. It is for **plot** reasons!) _Rarity can help with the outfits for us. Applejack can help with the food. Rainbow Dash can do something epic at the end to amaze every pony. I need you, Twily, to organize the wedding._

 _Thank you,_

 _Shining Armor._

Twilight read the whole letter aloud. Everyone was excited to help with the wedding, except for Bonnie. She once had nightmare about her brother leaving her because of his wife.

(XYZ 21 I believe if you want to know what I am talking about.)

"So, what do I do?" Bonnie asked.

"I guess help Twilight out." Rainbow Dash said, making Bonnie nervous.

"Don't worry sugar cube, everything will be alright!" Applejack said to Bonnie, making her smile a bit.

"This will be a blast, just you see!" Pinkie Pie said.

"Thanks guys." She said.

"Well, what are we waiting for darling? Let's head to Canterlot!" Rarity said, as the seven of them ran to the train station.

"So how long until we get there?" Bonnie asked.

"Awhile, sugar cube." Applejack told her.

"I guess I'll take a nap then." She said

"Okay, I'll wake you up when we're there okay?" Twilight told her.

"Okay." She said as she drifted off to sleep.

 _In her dreams..._

"Hello? Well this is new." Bonnie said as she walked around in dark room.

"Hello? Any pony here?" She asked, looking around.

" **Hello, young one.** " Some _thing_ said. Bonnie looked around before seeing it in darkness.

"Who or what are you?" She asked it.

" **I am that little darkness that is in us all. Sometimes I manifest or grow because of a certain emotion. But your case is different. You are a rare type, you see, I don't reflect on your emotions. No, I reflect on your behavior. I am little in you, but as you grow, I also shall grow. Even if you can never show me, you can always feel.** " It said, " **Just call me, Darkness**."

"Well, why are you telling me this now?" She asked Darkness.

" **Well, let's just say, you might want to be careful tomorrow. Okay? Okay. Bye bye!** " It said leaving Bonnie.

"In us all?" She repeated its words.

"Hey Bonnie wake up!" Twilight yelled, waking Bonnie up.

"Yea!" She said, as she jolted up from her nap.

"We're here!" She said as Bonnie ran.

"Let's go!" She said as she ran when the train stopped. Shining Armor was there when they arrived.

"Twily!" He yelled, seeing her and her friends.

"Don't you Twily me! You better explain to me why you didn't tell me sooner!" She said to him, enraged.

" _Wow, her aura is really red. Is she that mad? He must've been busy for Arceus's sake!_ " Bonnie thought.

"Twily, let me explain. We've been busy keeping the Changelings out. I've been using a protection spell to keep them away, but I don't know for how much longer." Shining Armor explained, making Twilight calm down.

"What are Changelings?" Bonnie asked.

"Changelings are creatures that can turn into any pony it sees. They can easily fool other ponies. The only thing they want is love." Shining Armor explained, making Bonnie afraid.

"Okay that sounds bad!" She said hiding behind Twilight.

"Wait I forgot, this is Bonnie. She's been staying with me. Celestia requested that she stays with me and my friends, for she said she has an unknown potential." Twilight told him.

"Wow, must be really impressive for someone like you." Shining Armor said to Bonnie.

"Hey! She said unknown." Bonnie said.

"Come on let's help make this wedding a reality!" Pinkie Pie said cheerfully, as she and the others went to do their jobs.

"So, who are you getting married to?" Bonnie asked rather curiously.

"Oh, her name is Cadence." Shining Armor answered her.

"Wait, you are getting married to the best foal sitter ever!" Twilight said happily.

"Getting married to the who now?" Bonnie asked.

"Cadence was the best foal sitter for me!" Twilight explained.

"Um, Okay." Bonnie said.

"Well, speaking of her, let's go see how she is doing." Shining Armor said as he lead them to their room.

"Oh, hi sweetie, how are you doing today?" She asked him.

"Good, I want you to meet one of Twilight's friends, Bonnie." Shining Armor said as Cadence walked over to her. Bonnie nervously looked back at Cadence , not knowing what she should do.

" _Her Aura is odd. I was expecting something different. Is she a Changeling? Can't be, can she? If so, then why is her aura so strong? I need to figure this all out later. Maybe as the day progresses, I find more evidence to back up my theory._ " Bonnie thought as Cadence walked away from her.

"Okay.." Bonnie said.

"Hey Cadence wanna go downstairs?" Twilight asked her.

"Sure, why not Twilight!" Cadence said. The three went downstairs to check to see how things were going.

"Hello Princess, how have you been?" Applejack asked offering some apple fritters.

"Good." She replied grabbing a fritter. She took a bite, pretended to like it. Then threw the rest into the trash.

"Oh no she didn't!" Twilight and Bonnie said at the same time. They both saw her put the fritter in the trash. Bonnie decided to go ahead. When she caught up with Cadence, she looked like she never saw the event happen. Twilight caught up eventually, knowing Bonnie was suspicious. When they were with Fluttershy and the birds, Cadence did like she did Applejack, minus the fritters.

Then when they were at Pinkie Pie's area, they were outraged.

"You like it?" Pinkie asked Cadence.

"Well, this is a party for four year olds!" She scolded her. Both of them went back to the room they were given, mad.

"You saw what I saw right? Cause if not I must be going crazy!" Bonnie began.

"I saw what you saw, it's unbelievable. This isn't her!" Twilight said. Bonnie then left the room and went to outside to see their friends, Twilight following a little later.

"Can anyone else agree that she isn't who she seems!" Bonnie started confusing everyone except Twilight.

"What are you talking about?" Rarity asked.

"Cadence, did you know how she acted?" Twilight continued. Everyone was confused, either they didn't notice, or that they just didn't care.

"What are y'all talking about?" Applejack asked.

"Did you know that she threw out your apple fritter after one bite?!" Bonnie asked, practically yelling.

"She was probably trying not to be rude, or an accident." Applejack said. Bonnie sighed calming down a bit.

"And Fluttershy, remember how she talked about the birds?" Twilight asked the timid pony.

"Well, one of them was singing off key." She said timidly.

"And, Gah!" Bonnie said falling.

"Don't stand in your chair!" Applejack said, catching Bonnie.

"I'll remember that." She replied getting back in it.

" _This is going to be harder than we thought._ " Twilight thought.

"I'm going to go inside. This day has been crazy for me." Bonnie said walking inside. Twilight trailed behind her, following her into their room. Bonnie senses Cadence's aura again, only for it to be more rough and violent toward her own. She immediately stopped sensing it. If she were to continue, she would have otherwise fainted.

"Okay, not going to do that again!" Bonnie said, speaking her thoughts.

"Do what?" Twilight asked.

"Uh, nothing..." Bonnie trailed off.

"Okay." Twilight said. Bonnie tried again, only to stop almost instantly.

" _Why is hers so strong? I can't even check it for a whole minute! If I were to, it would knock me out! Well, maybe because I'm at a distance, and that the first time wasn't as violent._ " Bonnie thought, laying down on the bed.

"Sigh, what do we do now Twilight? Twilight? Where are you going?" She asked the lavender pony.

"Oh, no where." She replied.

"I'm coming!" Bonnie yelled as she followed Twilight.

"Why did you follow me?" Twilight whispered to her.

"Well, I want to see what's going on too!" Bonnie whispered back. They looked into the room Shining Armor and Cadence were in, and saw something they couldn't unsee.

"Oh, my..." they both said. Cadence was draining Shining Armor's love, is what hey had seen.

"Okay, one thing that is not her!" Bonnie whispered to Twilight as they left the room.

"Right!" Twilight replied. Then they were both knocked out.

 _Hours later..._

Twilight and Bonnie woke up in a dark cave. Twilight used her magic to light up the dark area, only for them to see "Cadence's" face.

"Okay, now that is creepy!" Bonnie said.

"Well, this is an abandoned cave, so I doubt you'll ever be getting out of there." "Cadence" said.

"Um, you know I am just a filly, right?" Bonnie questioned her.

"That is not necessary. For yet you and your friend are in the way of my plan..." "Cadence" began before.

"I knew you were fake!" Bonnie yelled.

"Enough idiot! For yet now I need to take control of Equestria!" She finished before Twilight fires a magic beam, which bounced off the walls.

"Good luck!" She said before her face disappeared, and the rest of the room lit up. Twilight still had her magic charged, she was going to fire.

"Wait this is the real one!" Bonnie said getting in the way. Twilight was confused, until she looked at Cadence, noticing her scratches, scars, and bruises.

"Please don't hurt me!" She pleaded, covering her face with her hooves. Twilight stopped charging her magic, and instead walked over to the injured princess. Cadence looked up and saw who it was.

"Twilight..." she began.

"Cadence..." Twilight started

"Sunshine, sunshine, ladybugs awake, clap your hooves, and do a little shake!" They both said at the same time.

"You remember me!" Twilight said happily.

"Okay, first of all, what was that? And secondly, how do we get out of here!" Bonnie said. "Oh, hi."

"I think I know how." Cadence said as she ran in the cave. Bonnie and Twilight followed. Once they found a minecart, they hopped in and ride their way out.

"Wow, that was easy." Bonnie said.

"Let's hurry!" Cadence said, as the three started running towards the castle. Bonnie looked up and saw the bubble cracking.

"Uh, girls I think we might be too late for one thing." Bonnie said as she pointed up to the sky. Cadence and Twilight saw the cracking shield, which made all three of them hurry.

"Stop!" Cadence yelled as she entered the room. Everyone gasped, and looked at the real Cadence.

"This is an imposter!" Cadence yelled, making the fake surprised. While surprised, she grinned, then she started to change. The imposter changed into the infamous Queen Chrsylas!

"Ahahaha, so you finally figured it out. Well I don't need to play pretend much longer, for I have drained Shining Armor's love, and he is under my control. Not long will my minions come in and wreak havoc on this land, and all your love will belong to us!" Chrsylas said, as everyone gasped again. Then Celestia came in to stop her.

"Your plans will be stopped Chrsylas!" Celestia yelled sending a ray of her magic towards the shapeshifter. Chrsylas sent her ray of magic overpowering the Princess's and knocking her out.

"Celestia!" Twilight and Bonnie yelled, going to her aid.

"My my, with Shining Armor's love, my magic is stornger than Celestia's magic!" She said as she laughed manically.

"Go get the Elements of Harmony." Celestia said to the two.

"Let's go girls!" Twilight instructed, as the five ponies followed Twilight and Bonnie. When the seven ran outside, Changelings were everywhere.

"Oh boy." Bonnie said as they continued running.

"I think I can hold them off!" Bonnie said, suddenly feeling confident.

"What? But you can't!" Twilight said.

"You girls are the Elements. I'm not! The only thing I could do is help you keep them off!" Bonnie said.

"You'll get yourself killed!" Rainbow Dash yelled.

"Probably, but I won't without trying!" She replied.

"We have faith in you!" Pinkie Pie said as they left her.

"Good luck!" They all said.

"Thanks I'll need it." Bonnie said as she started fighting. It was 1 to 100, but she didn't care. She launched an aura sphere at them and it took out a severe amount.

"Alright! Let's try another one!" She said as she launched another one, this time getting twice as much as before. She then started running where her friends went.

"That'll do for now." She said as she continued back into the room she was in earlier.

"Where are they?" She asked as she then looked up, and saw them in cages.

"Oh great." She said.

"Why hello, have we met?" Chrsylas said as she appeared before Bonnie.

"I guess I'll have to fight on my own. Well here goes nothing!" Bonnie said, as she then felt a rush of energy. Something started surrounding Bonnie, and she then had beautiful butterfly wings, which couldn't be seen to the naked eye, and her blue eyes shined a tint of light blue ones. With that, she could use various abilities. She knew one thing, she _now_ had a fair fight.

"Alright, let's go!" Bonnie said as she fired of and Energy Ball.

 **Cliffhanger! Ah, I love doing that. But really I just gotta upload this. See ya in part two. Bye!**


	5. Saving Equestria Part Two: An Epic Fight

**Alright let's go with this one! Will Bonnie win? Find out now!! But one thing to note, what happens in this chapter _may_ surprise you. Let's dive in!!**

"Alright let's go!" Bonnie said as she launched and Energy Ball. It made a direct hit onto Chrysalis. (I just realized I spelt her name wrong in the last chapter. Well, just roll with it!)

"Gah!" She said as she got hit by the Energy Ball. Bonnie then got close to her and put her hoof on her chest. Then, Chrysalis was thrown against a wall, because of the Force Palm.

"Alright!" Bonnie said as she backed up. Then she noticed she was going back to her normal self.

"What happened?" She asked. Then she felt like she could barely stand.

"Take this, you little filly!" Chrysalis said as she launched a beam of her magic straight towards her. Bonnie took the hit, but not to well. She was flown back to the nearest wall, causing her to take great damage. Bonnie was in a tight spot, and didn't know what to do.

"You can do this!" Bonnie suddenly hears Pinkie Pie yell.

"We believe in you!" Rainbow Dash said.

"We know you can beat her!" Applejack yelled.

"Give it your best shot!" Rarity said.

"Don't give up!" Twilight yelled.

"Everyone believes in you!" Fluttershy yelled. Bonnie soon came to realize that _everyone_ believed in her. The fate of Equestria was in her hooves. She knew she _had_ to at least get her out of there.

"You know what, you're right! I will never give up!" Bonnie yelled as she felt the energy rush and grew the wings again, with her light blue tinted eyes.

"Let's see you take this!" She yelled, throwing an aura sphere this time, doing a greater amount than the Energy Ball.

"Take this!" Chrysalis yelled, sending another beam of her magic towards Bonnie. Bonnie blocked it with her shield.

"Now try this out!" She yelled throwing another two aura spheres.

"Gah! You know that hurts!" Chrysalis yelled.

Then Bonnie changed back again.

"How many times is that going to happen?" She asked under her breath. She then noticed a beam of magic coming her way, but it was too late to try and dodge.

"Woah!" She yelled, being thrown to another wall. At this point, she felt like giving in, but she wouldn't. Bonnie knew, she had to keep going, even if it would cost her, she knew she had to.

"I'm... not... letting... you... win!" She said as she got up.

"Well, you should, because I doubt you can stand up after my next one!" Chrysalis said. Bonnie didn't know if she was right.

"I... don't... care!"' Bonnie yelled. Then she tried to use an aura sphere in her normal form. It was small, however, due to her little energy.

"Try... this!" Bonnie yelled, launching the little aura sphere. When it hit, it did nothing.

"That tickled, do it again. I dare you!" Chrysalis said, as she chargered up another attack. Bonnie didn't know what to do at this point. She could barely move, her attacks did nothing, and there was no way to try to get back to _that_ form. Then she started glowing, as if she was changing into something else.

"What's going on now?!" Chrysalis said, enraged. Then the amulet on Bonnie's neck began to glow, going right in front of her, and spinning around her. Bonnie closed her eyes, as if she had done it before. Then moments later, when it went back to her neck, she looked like an alicorn!

"Equestria will not fall to your hooves!" She began. "For I am the seventh Element, COURAGE!"

"No, it's only a myth." Cadence said surprised.

"Take this!" She yelled, launching a large ball of pink energy. It managed to know Chrysalis and the rest of the Changelings.

"I will return and defeat you, stupid filly!" Chrysalis yelled.

"The name's Bonnie!" She yelled at the Changeling queen. Then she changed back to her normal form, still exhausted. Bonnie still managed to stand after that. She was very exhausted, she was panting at this point. Cadence got Twilight and the others out of the cage, and got Shining Armor out of his trance.

"W-what happened?" He asked when he was out.

"That'll be discussed later." Cadence told him. Meanwhile, Twilight and the others were helping Bonnie stand up, even with her failing almost every time. Celestia then came over to her.

"Yes Celestia?" Bonnie said looking up at the princess.

"I think it's about time you knew." Celestia stated.

"Knew what?" Bonnie asked.

"Come with me." Celestia said.

"Can they come?" Bonnie asked, pointing to Twilight and her friends.

"Sure." She replied.

"Hey Twilight, Applejack, Rarity, Rainbow Dash, Pinkie Pie, and Fluttershy! You guys can come!" Bonnie yelled to them. They came along with Bonnie, as they followed Celestia.

"So what is it that you wanted me to know?" Bonnie asked Celestia.

"You'll find out in a moment." Celestia replies to the filly. When Celestia found the room she was looking for, she opened the door. When it was opened it showed a room, filled with toys, a bed, and various other things.

"You were originally born in Equestria." Celestia said, surprising everyone pony.

"What?!" They all said in shock.

"Years ago, our mother Stacey, gave birth to you. We're unknowingly under attack at the time. When mom showed you to us, we were in love. She said what your name was, and that made you what we felt like the best sister ever. But when our father Alex came in, he told us we had to run. Apparently, while we were running, mom had lost you, she told Luna and I to run until we found an exit. When she found our father, well, the rest was history. We thought you died, a reason why that Luna became Nightmare Moon. This was unbeknownst to you. When Arceus told me that you were alive in his world, I was overfilled with joy that you were alive. He told me how you did everyday in there, and your journeys were amazing. But when he told me about your death in his world, I thought it was time that you returned. I told Arceus about you returning here, and he agreed. Though we thought it would be impossible to get you back here, we were mistaken. You were fine when you returned. As Arceus stated, you are one of the first chosen ones to come here." Celestia explained.

"Wow." Bonnie said.

"You're originally from here, but not at the same time. I don't get it." RD said.

"What she means is that, I was born here, but sent to another world for my safety." Bonnie explained to the confused pony.

"Wait, how come you haven't told us that?" Twilight asked her.

"Well, while I was taking those naps and sleeping at night, Arceus talked to me. He told me not to tell you until at a certain point. I guess that time was now." Bonnie said.

"I guess that makes sense." Fluttershy said.

"Shouldn't we be getting the wedding back up again?" Pinkie Pie asked.

"Let's do that." Celestia said as they went back to fix the wedding up again. When the wedding was fixed, everyone got into their seats.

"And do you, Princess Cadence, take Shining Armor as your husband, through sickness and until death." Celestia asked her.

"I do." Cadence replied.

"And do you, Shining Armor, take Cadence as your wife, through sickness and until death." Celestia asked him.

"I do." He answered.

"Now you may kiss the bride." Celestia states as Cadence and Shining Armor kissed. Everyone gave their cheers to the newly weds.

"Well, this has been an eventful time. Now hasn't it?" Bonnie asked her friends. Her and her friends chuckled at the thought.

" _Well now I know where I belong!_ " Bonnie thought.

 **Sigh, now I got this off of my shoulders, this is probably shorter than the rest, but I wanted to get this done for the most part. And I hope you have been surprised! Now to work on Sonic and Pokémon! See ya later. PokeGirl out!**


	6. Struggles With Thoughts, Applejack Knows

**So, I had some time off, and I am drawing some blanks for some stories and I felt like to update this one, despite it being one of those stories, where I drew a blank. But do not worry! I will start writing stories again soon! Just that this is the only thing that gathers my interest.**

 _Weeks After..._

Bonnie for some reason started having problems with her aura and magic. It all started a week after the wedding incident at Canterlot.

 _A few weeks back..._

"Hey Twilight!" Bonnie yelled, getting the lavender pony's attention.

"Yes Bonnie?" Twilight replied. Bonnie was recovering from the incident and just got released.

"Since now I'm out, think we could try some spells?" Bonnie asked as she hopped in place. (Basically pulling a Pinkie P-

Pinkie Pie: hey who are you?

Gah get outta here! I'm the author, and I was about to say something!

Pinkie: oh sorry! I'll leave you be!

 **Pinkie leaves.** That was a close one. Anyway you knew what I was going to say.)

"Alright, since you really done any, I guess it can only be fair." Twilight replied, Bonnie now excited.

"Yes!" She said. Bonnie was too hyper however, she realized that and calmed down.

"Come on Let's go!" Twilight said as they ran towards the house. Once they arrived at Golden Oaks Library, Twilight decided to try a certain spell with her.

"How about we try the teleportation spells?" Twilight asked her.

"Um, _spells_?" Bonnie replied.

"Oh, I forgot to tell you, there's normal teleportation, which is to where you teleport to where you're looking at. Then there's advanced, which is a certain area you teleport too, it isn't right in front of you." Twilight explained the two different teleportation spells.

"Oh, I wanna try the normal one first." Bonnie said as she processed the information she was just given.

"Okay, it's simple. Teleport right behind me." Twilight instructed.

"Okay, should be a piece of cake!" Bonnie said as she got her magic ready. But when she tried the spell, it didn't teleport her.

"Huh?" She said, confused.

"Try it again." Twilight told her. Bonnie got her magic ready and teleported this time, but out of the house!

"Uh Twilight." She said, knocking on the window.

"Oh, it may take a while to master. Maybe you should try again tomorrow." Twilight suggested.

 _Present Time..._

Ever since that day, Bonnie had trouble with control. With her more likely to go see Celestia half of the time.

"Sigh." She sighed. Bonnie wanted to try it again, but didn't want to risk _that_ again. She decided to take a nap, since she has been a little restless for the past two days.

"Hey Twilight, I'm gonna go take a nap." Bonnie told her as she went to her room.

"Okay, I'll wake you up in a bit okay." Twilight told her. Bonnie nodded and went to her toom. She got ready for her nap. It took her five minutes before she could finally go to sleep.

 _In her dream..._

"Hello?" She said as she walked around in the darkness.

"Remember me?" The Darkness said as it leapt onto her.

"Yes I remember you. Can you explain why I'm having trouble with my magic _and_ aura." She asked it. It just chuckled, and stood there.

"Oh there is a reason. Even if you don't know it, you are _fighting_ something in here." It explained as it chuckled again. Then it leapt onto her, this time more literally.

"It was a bad idea for you to come here!" It said as it tried to attack her. She dodged the attack, luckily.

"Alright, if it's a fight you want. Then it's a fight you'll get!" She said as she charged up her magic and launched it towards it. It took her attack, only for her to get hit by its attack and her being thrown similar to a wall.

"Bonnie wake up!" Twilight yelled.

"Yea!" She said as she got up.

" _It was just there a moment ago, how could it have disappeared! Well there is more to tell her anyways._ " Twilight thought as Bonnie got up.

"We gotta go to Celestia's castle in Canterlot. Celestia says we have to take a test." Twilight explained, making Bonnie worry.

"Um, I haven't studied for stuff like that. Or I haven't studied at all!" Bonnie told her.

"Maybe it isn't an actual test." Spike said.

"Well, let's go, come on you two!" Twilight said as she left the house.

"Hey wait for us!" They yelled. They ran towards the station, along the way, they got their friends. Once all eight of them got on the train to Canterlot. Bonnie began to worry. Applejack apparently noticed and went to go sit with her.

"Hey sugar cube, why are you worried?" Applejack asked her. Bonnie didn't want to answer the question.

"Uh, nothing really." Bonnie finally answered. Applejack senses something was up, so she stayed with Bonnie for a while. Bonnie looked almost annoyed, but at the same time comforted, knowing that she was going to supported all the way. Then she was confused, why was she annoyed when Applejack was sitting next to her. She didn't know how to answer it, so she just left it be.

"Sugar cube, you know you can tell any of us anything. Right?" Applejack finally spoke after the long silence between them. Bonnie didn't think of an answer for a while.

"I know." She finally answered.

"Why was that hard to answer for you?" Applejack asked her.

"I don't know." That answer came out quick. Bonnie was more focused on other things than Applejack's questions.

"I'm guessing you're worrying about something else than my questions." Applejack told her. Bonnie didn't answer that, she just stayed quiet. The silence between the two was long enough when Bonnie finally said something.

"Why are you asking me those questions?" She asked Applejack. Applejack thought of her answer before telling her.

"Well, I'm just worried for ya. That's all." Applejack explained. Bonnie gave her a hug after her answer. Applejack returned the hug, despite being surprised. Then the train stopped, realizing they had finally made it.

"Come on girls, let's go!" Twilight said as the eight of them got off of the train. They walked over to Celestia's castle. Once there, everpony else, minus Twilight, Spike and Bonnie, looked at the upcoming challenge for their friends. They nodded their heads in agreement, and the three went in. Once inside, they saw Celestia walking down the hall.

"Greetings Twilight and Bonnie." Celestia greeted them. They bowed before her, knowing of her loyalty.

"So what is this test we have to do?" Bonnie asked. She looked at Twilight as she had all the stuff she needed for a test.

"I have all my quills and enough paper to show my work!" Twilight said as she set her stuff down, accidentally spilling a roll of her paper.

"This is a different kind of test." Celestia said, as she rolled up Twilight's paper. "You will have to help the Crystal Empire."

"That's not in any of my books!" Twilight said flipping through her pages. Bonnie thought of that as something familiar, but ignored for as right then.

"It won't be, because it is rarely even known. Even my knowledge of it is very limited." Celestia said as she grabbed a crystal that was in a glass container. Then she placed the crystal on the floor, and used her magic on it, to reveal the Crystal Empire.

"But what I do know is that it contains a powerful magic. 1000 years ago, a unicorn named King Sombra, whose heart was as black as Night, took over the kingdom. He was ultimately overthrown, turned into shadow, and sent into the ice of the Arctic North. But not before he was able to put a curse on the kingdom, a curse that made it vanish into thin air." Celestia explained, as the crystal then made the Empire disappear. "If it is full of hope and joy, it will reflect all over Equestria. But if it filled with hatred and fear.." Celestia continued before turning the colorful crystal, making it black, and marking darker crystals appear from the ground.

"That is why I need your help. As I said, this is a different kind of test, but you can pass it. I believe in the both of you." Celestia finished as Twilight and Bonnie felt confident, of not failing the princess.

"We will not fail you Celestia!" Twilight said as she and Bonnie were about to leave.

"Bonnie." Celestia called her, as she stayed.

"You will need this however. Just so that way out can control your powers better while you are there. Make sure you where it at all times, because you will have no control over them if you don't have it. Okay?" Celestia said as she gave Bonnie a ring.

"Got ya sis, I won't let you down!" Bonnie stated as she gave Celestia a hug. Then Bonnie left, only to Twilight and the others ready to go.

" _I just hope she can do it without her fighting that."_ Celestia thought as she looked down the hallway.

Once everyone got back to the train station, everyone was surprised by what Twilight and Bonnie got as their test.

"Well, we can do it Twilight, I know we can!" Bonnie said trying to be encouraging, with more worry in her voice than anything else.

"Well, what if _we_ fail. Or what if _I_ fail?" Twilight asked the filly.

"Um, Twilight I doubt we will fail this. Should be a piece of cake!" Bonnie said.

"OOO! I like cake!" Pinkie Pie said.

"Uh, I gues you're right." Twilight said as they got onto their train.

"Hey RD, can come with me for a moment?" Applejack whispered to the rainbow pony.

"Okay, what is it about?" Rainbow Dash asked as her and Applejack got a table close to Bonnie.

"Well, Bonnie's been acting a bit... _different._ " Applejack stated.

"Are you sure, she seems fine to me." Rainbow Dash said as she looked over to see Bonnie, grabbing her heard with her hooves, as if she had a headache.

"Okay, you _may_ be right." Rainbow Dash said as she looked back at Applejack.

"Not _may_ , I _am_ right." Applejack corrected her friend as she looked at Bonnie, who was diagonal from the two mares. She kept grabbing her head, as if she was in real pain. Applejack then got a rare glimpse of her eyes. She lifted her head to see if anyone was watching. They looked saggy, not only that but bloodshot, as if she hardly had sleep. This wasn't the thing that sent chills down Applejack's spine. It was the color of her eyes. _Red_ , that was all they were. When Bonnie put her head back down, Applejack signaled Rainbow Dash to go with her to Bonnie's seat. She nodded and agreement, and followed the orange mare. One sat next to her, the other across from Bonnie.

"Hey is something wrong?" Rainbow Dash asked, getting goosebumps when she saw the filly's eyes.

"No, nothing to worry about." Bonnie said, chuckling nervously afterward. Applejack and Rainbow Dash got concerned for their young friend and wanted to help her, but could almost nothing.

"We should stay here, just so that way nothing bad happens to her." Applejack suggested.

"Yea we should, and did you see her eyes? They look terrible!" Rainbow Dash replied to the orange mare as she agreed with her statement. They looked at their friend, wondering what was wrong with her.

 _Screech!_

The train stopped, it was time to get off. Despite them still being saggy, Bonnie's eyes were no longer red nor bloodshot, like Applejack and Rainbow Dash saw earlier. The three got off the train. They walked over to Rarity to tell her what they saw.

"Oh Sweet Celestia, That is terrible!" She whispered to the two mares, looking at Bonnie.

"Yea, Ah can kinda agree." Applejack said, rubbing the back of her head with her hoof.

"Twilight!" They suddenly heard Shining Armor yell, getting everyone's attention.

"This way!" He yelled again, with them following him. They ran in the cold, with Bonnie worrying the most.

"How much longer until we're there?" Bonnie asked while panting.

"Just a little further." Shining Armor repliedAs then something tried to get them from behind. Whatever it was, whenever it shot it's magic, it threw Bonnie all the way to the front of them, with her luckily landing on her feet. This made the nine run faster.

"Go on, I'll try to hold him back!" Shining Armor suddenly yelled, as everyone kept running towards the now showing shield. Once they had entered, they felt relief. Then they realized that Bonnie was missing, only to appear right in front of them, still running.

"Bonnie wait!" They all yelled as they ran after her. She came to a stop when she saw Cadence.

"Bonnie... why were you still running?" Twilight asked before getting unexpectedly hugged by the now crying filly.

"Why are you crying darling?" Rarity asked as she went over to the filly. The only reply she got was sobbing and panting.

"That's a bit odd, if you were to ask me." Rainbow Dash said. Applejack nudged her, only for Rainbow to roll her eyes at the orange pony.

"I... I just need a break." Bonnie finally spoke, as she broke away from her hug with Twilight.

"A break from what?" Applejack asked. Bonnie then looked at Applejack, and for a split second, Applejack could've sworn she saw the red eyes again. It was if she was telling her to be quiet.

"Nothing, I just need one." Bonnie spoke after another long silence. Everyone looked at her confused, as Bonnie left the six, going up to a room that was in the castle. She found a bed in the room, luckily, and went to sleep on it.

" _Sigh, I just need rest, that thing is just to stressful to deal with. I'm guessing Applejack knows, other she wouldn't have asked that question._ " Bonnie thought as she went to sleep.

 **Sigh, this got Dark a little fast. So yea, what was stressing Bonnie out, and how does Applejack know? Why were her eyes red and bloodshot on the train? And why did she randomly hug Twilight? Found out tomorrow in _Dealing with Darker Forces._ Technically The Crystal Empire part two!**


	7. Dealing With Darker Forces!

**Alright, so this is part two! _Dealing With Darker Forces_ is here! Now, I will be gone next week cause I am going to hang out with some of my family, but I will get this and another chapter for another story out today. Well, I hope you enjoyed!**

Bonnie closed her eyes after being restless for the past few days. When she closed them, she felt relief, relief that she can finally sleep, and relief from **that**. She slept soundly for a couple of hours. Until...

"Hey Bonnie! Bonnie you gotta come quick!" Applejack yelled. This woke the little filly, her eyes blurred for a while before gaining full vision again. Bonnie walked out of the room, still a bit tired.

"What is it Applejack?" She asked the orange pony before yawning.

"Just follow me sugar cube." Applejack instructed, running downstairs. Bonnie followed, with everyone surprised by how she looked but said nothing about it. When she got down there, she saw Cadence in bad shape. Tired, like she was.

"Well, how can we help?" Bonnie asked, breaking the long silence they all had.

"Just keep the crystal ponies happy, otherwise, well you two know." Shining Armor said as Twilight and Bonnie nodded, knowing what he meant. The seven ponies left the castle.

"I think we should split up, see if we can any useful information about this place." Bonnie suggested. Despite her being tired, she could do some things. Everyone agrees and split up all over town meanwhile Bonnie stayed at the castle.

"Bonnie, aren't you going to go with them?" Shining Armor asked, coming into the castle.

"Uh, in a moment." Bonnie said, sounding suspicious. Shining Armor didn't notice the suspicion in her voice. She went upstairs, went into her room, and closed the door, locking it. Some dark mist began surrounding her body, for she closed her eyes. Struggling for a moment, before she opened her eyes, the mist disappearing, her eyes red like they were on the train.

"Heh, looks like she _finally_ gave in. Sigh such a shame." She spoke, in a deep tone. Bonnie wasn't in control anymore, for _it_ had taken over. (And no, King Sombra isn't taking control, it is a darker force!)

"Well, no will notice- right?" She said, changing her tone. She unlocked her door, and went downstairs, leaving the castle. She wore sunglasses so no one would notice her eyes. Bonnie was looking for Applejack, and eventually found her with everyone else.

" _Gah! That ruins everything!_ " She thought in the tone she spoke earlier.

"Oh, there's Bonnie!" Twilight said, running towards the filly. Twilight hugged the filly for a moment before asking some questions.

"Where were you? And why are you wearing those glasses?" Twilight asked her.

"Oh, uh, I was at the castle, getting something to cover my eyes. And uh, because the sun is to bright?" Bonnie replied, with her last answer sounding more like a question.

"Oh, okay." Twilight said as she and the others went inside, minus Applejack. Applejack walked up towards the filly noticing that something.

"Look, I don't know what you are, but you aren't going to mess with my friend!" She whispered to the filly.

"Sigh, well you're the only who has figured a part of what will happen out. But you don't know the rest. Now if you can keep this quiet, then I'll think about _it_. In the meantime, I suggest you keep your mouth shut, or else bad things will happen here. Got it?!" Bonnie whispered in the deep tone. Applejack paused for a moment.

"Wait what is _it?_ " She asked.

"I've said too much- let's get inside before suspicion arises." Bonnie said, changing her voice again. Applejack agreed this time, going in. They only they saw were books stacked on top of each other.

"Uh, what are you looking for?" Bonnie asked.

"We're looking for a book about the Crystal Empire's past." Twilight explained. Bonnie saw a book similar to Twilight's explaintion.

"A book like this?" She asked, showing the book to Twilight.

"Yes! Where did you find it?" Twilight asked the filly.

"Uh, I don't think that's important right now." Bonnie stated.

"I guess you're right. Anyway, we got the book! Let's see what they would do before King Sombra took over." Twilight said opening the book. Bonnie started walking backwards, getting away from the six. Applejack noticed and followed her. Bonnie didn't notice luckily. Bonnie found an alley near the Empire's exit. Applejack his behind a bush, just in time before Bonnie turned around, to see if she was being followed. With a second look back, she decided to flick her hoof. When she did, black magic showed, instead of the usual yellow that Applejack would see. Bonnie chuckled to herself, in that deep tone. She took the sunglasses off to reveal the red eyes she had on the train. With them now turning into a more darker red, she chuckled again as her whole body showed pitch black, before flashing back to her normal colors.

"Gah! She still isn't giving up, well, there is a way I will make her. _It_ just has to be complete before I am free. Heheheh." Bonnie spoke in the tone. As she was about to leave, Applejack made a break for it, without her noticing. Or at least she thought, for Bonnie heard Applejack's hooves hitting the road, and turned around to see if she was there. Lucky for Applejack, she ran just in time before she turned around. Applejack let out a sigh of relief and went to go regroup. Bonnie crept behind slowly. When Applejack made it back to the others, Bonnie did as well.

"Where were you two? We were just about to go look for you." Rainbow Dash asked the two.

"Uh, we went for a walk around here. It sure was nice. Wasn't it Applejack?" Bonnie said, nudging the orange mare who nervously agreed.

"Uh, yea, it's a really big place." Applejack said nervously. Rainbow Dash's suspension went away, as when she went to the others they sighed in relief. As they returned to the castle, Bonnie pulled Applejack over to a alleyway near it. Bonnie looked out to make sure no one else saw what was about to happen.

"We're you following me?" Bonnie asked in the deep voice, her eyes glaring red.

"No." Applejack lied.

"Yea right!" Bonnie yelled at her.

"I didn't, I swear to Celestia I didn't!" Applejack yelled back.

"Well, if you didn't, you wouldn't be yelling." Bonnie spoke calmly. She then dragged Applejack out of the alleyway, and into the castle. Applejack got up like nothing happened. She and Bonnie walked away from each other. Bonnie went upstairs, while Applejack decided to get caught up with Twilight and the others.

"So we need a crystal heart." Rarity said.

"Done!" Rainbow Dash said as she put the homemade crystal heart on the pedestal.

"Great! Now we just need everyone to be happy!" Pinkie Pie said as she got her things ready. Pinkie Pie left the others to gather other ponies, meanwhile the five that were left got food and games up so they could eat and do things. Meanwhile, Bonnie was upstairs, looking out the window.

"Hey Bonnie, won't you go help the others?" Shining Armor asked, surprising Bonnie. Luckily the glasses were still on her head.

"Uh, yes I will, I'm just gathering my thoughts." Bonnie said.

"Okay." Shining Armor said as he closed her door. Bonnie got up and locked the door before going back on to the bed in the room she was in. She flicked her hoof again, this time with the dark form staying two seconds longer than the last time.

" _Looks like she is figuring it out. As well as that Applejack pony. She could ultimately ruin my plans. That I do not know yet. For now I can only hope she doesn't._ " Bonnie thought as she got up and left the room. She went downstairs to see most of the Crystal ponies outside, enjoying their time.

 _In Bonnie's mind..._

"Ya!" Bonnie yelled, launching another aura sphere at the dark being in front of her.

"Why won't you get it that you can't win! Until I am out, you will struggle!" The being said as it launched another Dark Sphere towards Bonnie. Bonnie got hit and was thrown back, due to the force of the attack.

"Just let me do it, you will see soon enough why I need to be free!" It yelled at her as Bonnie got up.

"Unless if it's something good, then I won't let you!" Bonnie said, charging up her magic. When she let it go, it grabbed her attack, and turned it into its own. Then it launched her attack right back at her. She was once again thrown into a wall. She could barely stand after she that attack, as she struggled to stand.

"Well, now we're back to square one." It said. It chuckled as she continued to struggle to stand.

 **CLIIIIIIIIIFFFFFFFHAAAAAAANNNNNNGERRRRRRR! Yea this is threee parter XD. Anyway, what is the dark being's plan and what has to be completed in order for it to leave Bonnie's body? Why was Bonnie going completely black with dark red eyes? And why does _it_ think Applejack will get in the way of _its_ plans? Found out tomorrow in _Battling the Dark in Reality_! See ya next time! Peace!**


	8. Battling the Dark in Reality!

**Sigh, I am only doing this because I want to end the Crystal Empire stuff. Thing is though, this story may change to M, due to some chapters being very _violent_ , to say the least. Anyway, hope you enjoyed this ending! I will start another story about Season three to the end of season four I think, if not, then the beginning. This is going to be VERY long! See ya later peace!!**

"Well, feel like giving up?" The dark being asked, charging up another attack.

"No! I won't, why should I anyway?!" Bonnie asked charging her own attack. The two launched their attacks, colliding with each other, only for them to go through each other, hitting the other pony.

"Huh, one reason for your question. _This!_ " It said on a violent tone, as it tackled Bonnie, using its on version of her aura sphere at close range. It then jumped away, landing on its feet. Meanwhile, Bonnie struggled to stand up after that.

" _Now_ , will you let me do it?" It asked.

"Scoff, what do you think?" Bonnie asked, getting up. She ran towards the pony, and put her hoof on it. Then it was suddenly thrown back to the wall nearby (wait since when did your mind have walls? Oh well, plot reasons anyway.). It then got up on its hooves, as it teleported right in front of Bonnie. It put its hoof on her chest. Like what happened to it, Bonnie was thrown back against the wall, causing her greater damage than she did to it.

 _Out in the Empire._

Twilight and her friends were getting everything ready for the festival. Applejack was worried, wondering what was taking Bonnie so long.

"Ah'm gonna check on Bonnie, cause Ah'm wondering what's take her so long." Applejack announced. Twilight gave her a nod, as Applejack went upstairs to Bonnie's room. She knocked on the door, with no response.

"Hello? Bonnie, it's me, Applejack, Ah'm checking on you sugar cube." Applejack stated, knocking on the door again.

"Sigh, come in!" Bonnie said in a cheerful tone, before unlocking the door. Applejack entered, only to see Bonnie with a, problem.

"Oh sweet Celestia what happened?!" Applejack asked, seeing the figure in front of her. It was pure black, only with the exception of its eyes being white, and its pupils being red.

"It should be _me_ you should be asking." It said, in its deep tone.

"I am no longer in your mind Bonnie, now I am physical, and I like to you _and_ your friend to a secret area. Hmm hmm hmm." It said as it grabbed the two, before teleporting. As for Twilight and the others, they were getting everyone's spirits up. Everyone was happy as they played games, ate food, and watched some jousting.

"Hey, What's taking Applejack so long, she should be back by now." Pinkie Pie asked, with her friends noticing Applejack wasn't back.

"Well, maybe she's talking to Bonnie darling, you know she hasn't left Twilight's house a lot before coming here, right?" Rarity replied to the curious pink pony.

"Fair point, but she should be back by now!" Rainbow Dash objected, almost telling her statement.

"Well, maybe we should go check on them." Fluttershy suggested timidly.

"Well, some of us should stay down here, while the rest goes up and checks." Twilight stated, with her friends nodding in agreement.

"I think me, Fluttershy, and Pinkie Pie stay down here, while you and Rarity go up and see what the hat is going on!" Rainbow advised.

"Well, does anypony object?" Twilight asked, with no one saying anything.

"Okay, then it's official. Come on Rarity let's go." Twilight said, running off.

"Oh! Wait up darling!!" Rarity exclaimed, following the lavender pony.

"In the meantime, let's keep them busy." Rainbow Dash said, as the three got back to the hundreds of Crystal ponies. (Btw do know that there is a REAL crystal heart, and they have been told of its whereabouts, but after they checkup, well, nothing else to be said.)

Twilight and Rarity ran upstairs o the room Bonnie and Applejack were at, only to find the door locked.

"Why's the door locked?!" Twilight asked, practically yelling.

"Calm down darling, it's probably for privacy between the two. If I were checking on Bonnie, I too would lock the door." Rarity explained to the lavender mare, who calmed down.

"Alright, we'll just tell them that they're still talking." Twilight compromised. Rarity nodded and went downstairs with the lavender pony, looking back at the before going into her thoughts.

" _Wait, we should've knocked, to see if they were in there._ " Rarity thought. She shook the thought of, however.

" _No, let them have their privacy, it would be rude anyways._ " Rarity thought as she and Twilight proceeded to walk downstairs.

 _Meanwhile with Bonnie and Applejack._

"Ow!" Bonnie said getting up. Apparently when they teleported, they were two feet off the ground, and fell. Despite it not hurting much, the impact still hurt.

"Uh, care to explain where we are sugar cube? And speaking of explaining, what the jay was going with the red eyes, deep voice, and all that stuff!" Applejack asked. Bonnie was confused for a moment, but then realized what the orange pony was talking about.

"Oh yea, about that. Heh heh. Uh..." Bonnie tried to explain, but found herself at a loss of words. Applejack realized she was pressuring the young pony, who then felt sorry for her sudden outburst on her.

"Look, sorry Ah yelled like that. I was wanting answers." Applejack apologized, making the young pony stare at her. Bonnie only nodded, before looking at their surroundings.

"So, you two are up? Not surprising." Someone spoke, making. Bonnie and Applejack back into each other.

"Who the hay are you?!" Applejack question, her yelling in the darkness.

"Just call me, Darkness." It said coming out in front of the orange pony. "Boo!"

"Okay that sounds like a cheap name for someone like you!" Bonnie admitted.

"Oh shut it! What else would be menacing for someone who is literally a pony that is _dark_?!" It yelled, emphasizing on the word dark.

"Anyway, move orange pony, or I'll make you!" It said in a threatening voice. But Applejack stood her ground.

"And why should Ah?" She asked. Before Applejack could react, the dark pony grabbed a hold of her and threw her across the room. Applejack got the wall hard, and could barely stand.

"Now with her out of the way. Let's go!" It said charging up its magic. The next thing Bonnie knew, she was hit the pony's magic, only it was twice as powerful than earlier. Bonnie stood, however, knowing she couldn't give up. Bonnie charged her own attack, releasing It moments later. The dark pony couldn't dodge the attack like earlier. It hit hard, but not as hard as it's attack. As it was being to confident, it was suddenly hit with a powerful aura sphere. Apparently Bonnie was charging a aura sphere at the same time she released her magic.

"Clever." It admitted, standing up. It then did what it did earlier, it tackled Bonnie, and then launched an aura sphere at close range. Bonnie could barely stand after that. The pony then laughed, knowing that she was weak. Unbeknownst to it, Applejack tackled it and got on top of it.

"Gah! What are you doing?!" It asked her, confused.

"Helping my friend!" She yelled at it, before being thrown off it. Then it got hit by Bonnie's aura sphere.

"Gah! This is unfair! It's a 2v1!" It whined. They were surprised by its whining, what they didn't know was that it was a trick. Bonnie got closer, before she knew it, it put its hoof on her chest, and she was suddenly thrown back to another wall. She realized it was a trick.

"Uh, nice acting?" Bonnie said before chuckling nervously. She then got up and ran towards it, doing what it had just done. It got up, before launching a beam of magic almost instantly. As it was heading towards Bonnie, Applejack got pushed her out of the way and took the attack instead.

"Applejack!" Bonnie yelled, running to her side. Applejack had some kind of static coming out of her, as she twitched every few seconds. Bonnie was in tears, to see her friend in the state she was in. Bonnie then turned around, with her head down, still crying. Even though it couldn't be heard, it could be seen. Bonnie stood there, silent. The pony was confused, not knowing what she was planning. The dark pony walked foward, oddly concerned for the young filly.

"Are you okay..." it asked, trailing off. Next thing it knew, it was thrown against the wall, _hard_.

"YOU THINK YOU CAN JUST HURT MY FRIEND LIKE THAT?!" She yelled, enraged. Bonnie was in a state of anger, she wasn't thinking clearly.

"So now its a real fight?!" It yelled back. Then it suddenly got hit by a strong aura sphere. Red aura was surrounding her, indicating she was angry. Bonnie ran up to the pony and put her hoof on it, it was thrown violently against the wall. _It_ was now the weak one. Bonnie was in a state of mixed emotions, anger, sadness, and pain. Why she felt was unknown, but she did know why she felt anger and sadness. Bonnie then stopped attacking. The dark pony was confused, but dared not to get closer. Then Bonnie started crying softly, not knowing what was going, or what to do. She stood there, just crying.

" _Wow you are just a big crybaby._ " Diamond Tiara's voice rang in her mind. The dark pony stopped attacking as well, and instead, walked forward. It then tried to comfort Bonnie, who rejected its efforts. The dark pony knew why she rejected, but it knew it wasn't it's own fault. Applejack got in the way of the attack. The dark pony tried again, despite what it had done. Bonnie looked up to the dark pony, caring for her. Bonnie was confused, why was it comforting her. She then thought it was a trick, then she charged up attack and launched it. The dark pony was thrown back. The dark pony thought there was no point in helping her, so it attacked. But before it launched its attack, Bonnie walked over to Applejack. It stopped its attack, as it was something telling it not to. It tried again, only for to get the same result. (Btw while all this was happening, the thing with crystal heart and all was happening, but I don't feel like telling that, despite that making the chapter longer. But I am lazy to write that rn, maybe later.) It walked up to her again, this time with it trying to help. Bonnie, once again, rejected its help, and hit it with her magic. It gave up on helping the young pony. Then it decided to do something that would help, getting them out there.

"Hey listen, can I at least get you two out of here?" It asked. Bonnie looked at it for a moment, then nodded.

"See ya later." It said as got the two out of there. Apparently, it came with them. The three were outside the room. The dark pony went downstairs with Bonnie. Bonnie this time accepted it, knowing that this would probably be the only time it'd help. Before they got down there, the dark pony healed Applejack. She got up, only to be hugged by Bonnie. Then they looked at the dark pony, who just nodded, and left. Then they went downstairs, surprised to see the Empire safe.

"There you two are!" Rainbow Dash said.

"You two missed the most awesome thing ever!!" Pinkie Pie exclaimed.

"It was amazing." Fluttershy said timidly. Everyone laughed, along with Fluttershy, at the pony's timidness.

"I think its about time we got home, it's been a long day, and I'd like to rest!" Bonnie said, as everyone agreed, giving their goodbyes and farewells to everyone at the Empire. As soon as they boarded the train Bonnie and Applejack went to sleep.

"I wonder what _they_ did." Rainbow Dash said, as everyone chuckled at her question. Moments later, or as it felt like to Applejack and Bonnie, they arrived in Canterlot. Twilight and Bonnie suceeded the mission, and proved to Celestia and Luna that they are almost ready!

 **And that ends this! Now if you'll excuse me, I have to write another chapter for Aura Guardians. Anyway hope you enjoyed! This was gonna go out differently, but this suited it better. Now with this complete, time to get some season three up in the next story. Until then, see ya next time! Bye!**


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